Several possibilities. I had a couple of malfunctions showing up like this on my E60.
1. Your Mechatronic (Valve body) is failing. Needs new solenoids and a general maintenance.
2. Your tranny oil hasn't been changed. Forget what the manufacturer say about the oil being a life time oil. You need to replace the plastic sump which is actually an oil filter. But in this case when it's dirty it's probably clogged up your solenoids as well which will require cleaning and general maintenance.
3. If your tranny overheat, you may have clutch lining failure. The whole tranny needs to be serviced. Not cheap. Probably better to just look for a used unit and installed that in.
For no.3 that's what I did.
I busted my tranny because one time it had an oil leak via the heat exchanger (See pic below). Oil leaked into the radiator system. I replaced the radiator and cleaned the cooling system as well as changed the heat exchanger unit. But what I didn't realised was that the water from cooling system also went into the automatic transmission (albeit a small amount) mixing with the tranny oil. The moisture overtime ate into the clutch lining.
Hope the info helps and do report back on what you did to fix the transmission malfunction warning.
EDIT: Forgot to ask if your car is Auto or Manual. Mine is Automatic.